The acting commissioner of the Metropolitan police has walked into a political minefield just hours after taking over the reins from Sir Ian Blair.

Sir Paul Stephenson, who was hotly tipped to get Blair's job, was in effective charge at Scotland Yard when the decision to arrest Damian Green was made.

Perhaps aware of the sensitivity, he contacted the mayor of London, Boris Johnson, before the arrest. Now facing the fury of the Conservatives, Stephenson is getting an early taste of why Blair said the Met commissioner needs to have "copper- bottomed trousers".

Scotland Yard rejected Tory claims that anti-terrorist officers had been used to arrest Green and accusations from Nick Clegg, the Liberal Democrat leader, that counter-terrorism powers were invoked.

"That is nonsense," one police source said.

The officers involved were members of what was once known as Special Branch, and operate within the Specialist Operations directorate, which contains the counter-terrorism and security command. Police said Special Branch officers have always been used to investigate allegations of government leaks and there was no question of any counter-terrorism laws being invoked or anti-terrorist officers being used.

The source said that for obvious operational reasons the police could not inform someone in advance that they were about to be arrested. It is understood that officers are examining a computer and emails.